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Evolution of web services in bioinformatics

P. B. T. Neerincx
2005 Briefings in Bioinformatics  
This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited  ...  Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects.  ...  THE FUTURE OF WEB SERVICES IN BIOINFORMATICS SOAP-based web services and centralised systems both have their strong points and therefore both might face a bright future, in which they can live happily  ... 
doi:10.1093/bib/6.2.178 pmid:15975226 fatcat:alotxt4xurbbxavufbwrm6k6my

Bio-Sense: A System for Supporting Sharing and Exploration in Bioinformatics Using Semantic Web Services

Athman Bouguettaya, Mark Hepburn, Qing Liu, Kai Xu, Ji Zhang
2008 2008 IEEE Fourth International Conference on eScience  
Semantic Web Service for Bioinformatics Provenance The Genome Tracker project at ICT Centre Hobart is developing a semantic web services-based system for bioinformatics.  ...  The management of provenance-which refers to the evolution of information (i.e., from where and how the information is obtained)-is still in very early stage in these systems.  ...  Semantic Web Service for Bioinformatics Provenance The Genome Tracker project at ICT Centre Hobart is developing a semantic web services-based system for bioinformatics.  ... 
doi:10.1109/escience.2008.95 dblp:conf/eScience/BouguettayaHLXZ08 fatcat:s6l5mkznmbdf5bai4infpiv3y4

Bioinformatics activities at the University Hospital San Martino IST in Genoa

Paolo DM Romano
2017 EMBnet journal  
IST Bioinformatics Web Services (IBWS) A suite of WSs -the IST Bioinformatics Web Services (IBWS) (Zappa et al., 2010) -was developed to make databases available at the IRCCS San Martino IST accessible  ...  Bioinformatics Web Enactment Portal (BioWEP) The use of WMSs can be difficult for the majority of biologists. Web portals can allow users to enact useful workflows in a friendly environment.  ... 
doi:10.14806/ej.23.0.884 fatcat:x534vlgbezcd5mainfea57cylu

An Agent-Based Multilayer Architecture for Bioinformatics Grids

E. Bartocci, D. Cacciagrano, N. Cannata, F. Corradini, E. Merelli, L. Milanesi, P. Romano
2007 IEEE Transactions on Nanobioscience  
Bioinformatics BMC Bioinformatics Journal of Computational Biology Computational Biology and Chemistry Briefings in Bioinformatics IEEE Trans. Comp. Biol.  ...  • It is difficult to track the evolution of a research area • It is not existing any classification schema for bioinformatics resources • For the bioinformatics domain is not existing any classification  ...  into a MAS •Bioinformatics services and applications are wrapped by service agents  ... 
doi:10.1109/tnb.2007.897492 pmid:17695749 fatcat:32ogekykr5aspfkavite3oufc4

Open Bioinformatics

D. C. Jamison
2003 Bioinformatics  
Evolution of WWW protocols has given us a much better approach. Software applications that are not being distributed as source code can be implemented as a set of web services.  ...  The primary technology standards for creating web services are XML and SOAP. XML is the acronym for eXtensible Markup Language, and in structure XML is a superset of HTML.  ... 
doi:10.1093/bioinformatics/btg214 pmid:12691978 fatcat:er26ndsebje5nltbynacnz5bo4

A new Ontology Lookup Service at EMBL-EBI

Simon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson
2015 Workshop on Semantic Web Applications and Tools for Life Sciences  
The OLS has been reengineered in order to accommodate the OWL standard and provide a wider range of ontology-based services to the community.  ...  One of the major shifts has been the increasing use of the W3C Web Ontology Language (OWL) for representing biomedical ontologies.  ...  3) Web services for querying the structure of the ontology 4) A user interface for exploring and visualising the ontologies 5) A versioning system to track ontology evolution.  ... 
dblp:conf/swat4ls/JuppBLP15 fatcat:wmub2ck7xrcbzmzcl7djapy7g4

COnto–Diff: generation of complex evolution mappings for life science ontologies

Michael Hartung, Anika Groß, Erhard Rahm
2013 Journal of Biomedical Informatics  
to determine basic and compact diffs using matching and rules • Supported changes: merge, split, addSubgraph, move, ... • Web GUI and web service interface available • Multiple input possibilities • Support  ...  Rahm: CODEX: Exploration of semantic changes between ontology versions.  ...  Rahm: COnto-Diff: Generation of Complex Evolution Mappings for Life Science Ontologies. Journal of Biomedical Informatics (In Press), 2012 [3] M. Hartung, T. Kirsten, A. Groß, E.  ... 
doi:10.1016/j.jbi.2012.04.009 pmid:22580476 fatcat:lesy3bmhjvbbpn2jvzpdhpilaa

Bringing Web 2.0 to bioinformatics

Z. Zhang, K.-H. Cheung, J. P. Townsend
2008 Briefings in Bioinformatics  
In this report, we discuss the potential of Web 2.0 technologies to transcend this model and enhance bioinformatics research.  ...  We discuss lessons from information technology, predict the next generation of Web (Web 3.0), and describe its potential impact on the future of bioinformatics studies.  ...  BRINGING WEB 2.0 TO BIOINFORMATICS What is Web 2.0? We have only one World Wide Web. Web 2.0 is not a new Web, just a convenient term reflecting the evolution of the Web.  ... 
doi:10.1093/bib/bbn041 pmid:18842678 pmcid:PMC2638627 fatcat:cjpbzmxuzjcvhhekmykgisj5zi

ExPASy: SIB bioinformatics resource portal

P. Artimo, M. Jonnalagedda, K. Arnold, D. Baratin, G. Csardi, E. de Castro, S. Duvaud, V. Flegel, A. Fortier, E. Gasteiger, A. Grosdidier, C. Hernandez (+9 others)
2012 Nucleic Acids Research  
The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions  ...  Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics  ...  ACKNOWLEDGEMENTS We thank the Steering Committee of the Web Team for the support: Ron Appel, Lydie Bougueleret, Fre´derique Lisacek, Irene Perovsek, Torsten Schwede, Christian von Mering and Ioannis Xenarios  ... 
doi:10.1093/nar/gks400 pmid:22661580 pmcid:PMC3394269 fatcat:inyuly6vfje23h6xgsbn73ib5q

REMORA: a pilot in the ocean of BioMoby web-services

S. Carrere, J. Gouzy
2006 Bioinformatics  
Emerging web-services technology allows interoperability between multiple distributed architectures.  ...  of predefined workflows and a survey system.  ...  ACKNOWLEDGEMENTS The authors thank Clare Gough and Thomas Faraut for feedback and helpful comments on the manuscript and the Bioinformatics platform of the Genopole Toulouse Midi-Pyrénées for technical  ... 
doi:10.1093/bioinformatics/btl001 pmid:16423924 fatcat:amdttdyugzeibijmov33tqiqti

A Bioinformatics Reference Model: Towards a Framework for Developing and Organising Bioinformatic Resources

Hong Liang Hiew, Matthew Bellgard, Tuan D. Pham, Xiaobo Zhou
2007 AIP Conference Proceedings  
This paper presents an overview of the different functions and needs of bioinformatics stakeholders to determine what may be required in a community-wide framework.  ...  The relevance of this reference model to the bioscience research community, and its implications in progress for organising our bioinformatics resources, are discussed.  ...  hosted in over 35 countries with web-based bioinformatics tools [5] .  ... 
doi:10.1063/1.2816640 fatcat:r3srvwywyfedbgvatmwzpodnlq

Development of Bio-Metadatabase and Its Applications

Tomonori SUZUKI, Satoru MIYAZAKI
2009 Joho Chishiki Gakkaishi  
We also expect that Bio-metadatabase will be a core resource to design the semantic Web services and allow us to create user-oriented work-benches for bioinformatics data analysis.  ...  In this paper, we described various aspects of our Bio-metadatabase and some ideas with this database such as the one-stop query data retrieval system from multiple sites and the workbench for evolutional  ...  We also expect that Bio-metadatabase will be a core resource to design the semantic Web services and allow us to create user-oriented work-benches for bioinformatics data analysis.  ... 
doi:10.2964/jsik.19-92 fatcat:nxm67pg2bjaebpl3b6w6madugi

Bioinformatics research in the Asia Pacific: a 2007 update

Shoba Ranganathan, Michael Gribskov, Tin Tan
2008 BMC Bioinformatics  
We also thank the BMC Bioinformatics Editorial Office for their support and encouragement in making this issue possible.  ...  This article has been published as part of BMC Bioinformatics Volume 9 Supplement 1, 2008: Asia Pacific Bioinformatics Network (APBioNet) Sixth International Conference on Bioinformatics (InCoB2007).  ...  Evolution and phylogenetic analyses The evolution of genes, especially in response to pathogenic attack, is a complex process.  ... 
doi:10.1186/1471-2105-9-s1-s1 pmid:18315840 pmcid:PMC2259402 fatcat:lsxs6laimrbthpfdccswdf5pve

Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory

M. D. Brazas, J. T. Yamada, B. F. F. Ouellette
2009 Nucleic Acids Research  
In particular, the authors would like to acknowledge all of the contributors to the Bioinformatics Links Directory for their valuable input and suggestions for improvements to the directory; these individuals  ...  The Bioinformatics Links Directory is a community resource built on this commitment to the spirit of open access.  ...  Accordingly, web servers introduced in the 2009 NAR Web Server Issue include several specialized web service interfaces such as (Table 1) , addressing the need and introduction of new resources that  ... 
doi:10.1093/nar/gkp531 pmid:19528072 pmcid:PMC2703910 fatcat:45uzfpt6vrhgdi7wbm5rrsnnsy

DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins

A. D. Moore, A. Held, N. Terrapon, J. Weiner, E. Bornberg-Bauer
2013 Bioinformatics  
It provides a simple user interface with access to domain annotation services such as InterProScan or a local HMMER installation, and can be used to compare, analyze and visualize the evolution of domain  ...  DoMosaics is an application that unifies protein domain annotation, domain arrangement analysis and visualization in a single tool.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btt640 pmid:24222210 fatcat:zx7n7jzw3bggzirlo34uz7d7gq
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